Greetings,
So the first rising edge of the REQ line (when re-starting the transfer) is not the first clock edge? I guess there is a period after starting the operation and before the REQ clock starts that the REQ line is high?
One thing I would suggest would be to look at the start-up state of the control lines on the PCI-6534. You can pull-up or pull-down the control lines by connecting the CPULL pin to either the +5V pin or a ground pin. Try connecting the CPULL pin to ground. This pin is for controlling the power up state of all of the control lines.
Hopefully this will help.
NI 653x User Manual
http://digital.ni.com/manuals.nsf/webAdvsearch/EDE443F5C700373A862569B90072D26F?OpenDocument
Regards,
Todd D.
NI Applications Engineer